rimM Resolved · high auto-curated
H37Rv Rv2907c · MTBC0 mtbc0_003089 ·
176 aa · 3237190–3237720 (-) ·
RefSeq NP_217423.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 16S rRNA processing protein RimM |
|---|---|
| MTBC0 PGAP re-annotation | ribosome maturation factor RimM |
| Revised (this work) | Ribosome maturation factor RimM. Pfam: RimM (PF01782.25), PRC (PF05239.22), PRC_RimM (PF24986.2). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WH19
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Ribosome maturation factor RimM |
| Curated function | An accessory protein needed during the final step in the assembly of 30S ribosomal subunit, possibly for assembly of the head region. Essential for efficient processing of 16S rRNA. May be needed both before and after RbfA during the maturation of 16S rRNA. It has affinity for free ribosomal 30S subunits but not for 70S ribosomes. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | rimM |
| eggNOG description | An accessory protein needed during the final step in the assembly of 30S ribosomal subunit, possibly for assembly of the head region. Probably interacts with S19. Essential for efficient processing of 16S rRNA. May be needed both before and after RbfA during the maturation of 16S rRNA. It has affinity for free ribosomal 30S subunits but not for 70S ribosomes |
| Orthologous group | COG0806 |
| KEGG orthology |
K02860
|
| Gene Ontology (2) |
GO:0008150, GO:0040007
|
Orthology-based transfer (eggNOG 5.0.2, diamond). EC/KO/GO/CAZy are computed annotations, not manual curation; cross-check against the primary literature before treating a specific reaction as established.
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | 0.087 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 1 missense, 0 nonsense, 0 frameshift |
pN/pS from segregating SNPs (singletons removed) normalised by possible sites. Low pN/pS = purifying selection (a strong signal that a "hypothetical" is a real, constrained gene). A high pN/pS is ambiguous: relaxed constraint or positive selection (drug resistance, antigenic variation) inflate it; e.g. rpoB/katG/pncA score high here for resistance, not loss of function. A clonal disruption (one allele over a clade) suggests lineage pseudogenisation; a convergent one (many independent alleles) is typical of resistance loss-of-function.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
RimM | PF01782.25 | 1.1e-19 | 4–92 | RimM N-terminal domain |
PRC | PF05239.22 | 5.9e-13 | 101–173 | PRC-barrel domain |
PRC_RimM | PF24986.2 | 2.0e-14 | 106–172 | RimM PRC barrel domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: trmD (tRNA (guanine-N1)-methyltransferase), high confidence from genomic context alone (score 985 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2906c trmD |
tRNA (guanine-N1)-methyltransferase | 989 | 985 ctx | neighborhood:882 coexpression:875 |
Rv2909c rpsP |
30S ribosomal protein S16 | 979 | 973 ctx | neighborhood:812 coexpression:863 |
Rv1307 atpH |
ATP synthase subunit b/delta | 976 | 968 | coexpression:962 |
Rv0705 rpsS |
30S ribosomal protein S19 | 968 | 967 | coexpression:778 experimental:857 |
Rv2908c hyp |
hypothetical protein | 960 | 959 ctx | neighborhood:872 coexpression:692 |
Rv2904c rplS |
50S ribosomal protein L19 | 920 | 895 | coexpression:853 |
Rv3443c rplM |
50S ribosomal protein L13 | 880 | 871 | coexpression:860 |
Rv2890c rpsB |
30S ribosomal protein S2 | 897 | 867 | coexpression:859 |
Rv0702 rplD |
50S ribosomal protein L4 | 862 | 863 | coexpression:863 |
Rv0053 rpsF |
30S ribosomal protein S6 | 879 | 861 | coexpression:861 |
Rv0641 rplA |
50S ribosomal protein L1 | 859 | 860 | coexpression:860 |
Rv0682 rpsL |
30S ribosomal protein S12 | 871 | 857 | coexpression:857 |
Rv0701 rplC |
50S ribosomal protein L3 | 853 | 854 | coexpression:854 |
Rv0651 rplJ |
50S ribosomal protein L10 | 872 | 853 | coexpression:817 |
Rv3458c rpsD |
30S ribosomal protein S4 | 853 | 853 | coexpression:853 |
STRING combines evidence channels (neighborhood, fusion, cooccurrence, coexpression, experimental, database, text-mining) into a 0–1000 score. The ctx badge marks edges carried by the genomic-context channels (conserved neighborhood, fusion, phylogenetic co-occurrence), which are independent of orthology and structure and the strongest signal for an unknown gene. The no text-mining column recomputes the score from data alone, so a link that does not depend on the literature is visible. Association is a function hypothesis, not proof: corroborate with the operon context and the primary literature before assigning a function.
Evidence
- Legacy H37Rv annotation: 16S rRNA processing protein RimM
- MTBC0 PGAP product: ribosome maturation factor RimM
- Pfam (hmmscan --cut_ga): RimM PF01782.25 (E=1e-19), PRC PF05239.22 (E=6e-13), PRC_RimM PF24986.2 (E=2e-14)
- (auto-curated by rules from PGAP + Pfam + Foldseek; not hand-reviewed)
Sources
- Ancestral sequence & coordinates: Harrison LB et al. (2024), An imputed ancestral reference genome for the MTBC, doi:10.1101/2023.09.07.556366
- Product annotation: NCBI PGAP on MTBC0; legacy from H37Rv NC_000962.3 (RefSeq NP_217423.1)
- Domains: Pfam-A via hmmscan --cut_ga — RimM (PF01782.25), PRC (PF05239.22), PRC_RimM (PF24986.2)
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Controlled vocabulary: eggNOG-mapper 2.1.12 (Cantalapiedra et al. 2021,
doi:10.1093/molbev/msab293), eggNOG 5.0 DB
(Huerta-Cepas et al. 2019) — OG
COG0806 - Curated reference: UniProt P9WH19 (SwissProt, reviewed; Evidence at protein level)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
123 functional partner(s); context anchor
trmD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003089|Rv2907c|rimM MELVVGRVVKSHGVTGEVVVEIRTDDPADRFAPGTRLRAKGPFDGGAEGSAVSYVIESVRQHGGRLLVRLAGVADRDAADALRGSLFVIDADDLPPIDEPDTYYDHQLVGLMVQTATGEGVGVVTEVVHTAAGELLAVKRDSDEVLVPFVRAIVTSVSLDDGIVEIDPPHGLLNLE